Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

On the statistical mechanics of prion diseases

We simulate a two-dimensional, lattice based, protein-level statistical mechanical model for prion diseases (e.g., Mad Cow disease) with concommitant prion protein misfolding and aggregation. Our simulations lead us to the hypothesis that the observed broad incubation time distribution in epidemiological data reflect fluctuation dominated growth seeded by a few nanometer scale aggregates, while much narrower incubation time distributions for innoculated lab animals arise from statistical self averaging. We model `species barriers' to prion infection and assess a related treatment protocol.Comment: 5 Pages, 3 eps figures (submitted to Physical Review Letters

Particle size effects in the kinetic trapping of a structurally-locked form of a flexible metal-organic framework

First published online 08 Feb 2016The application of metal-org. frameworks (MOFs) for gas storage, mol. sepns. and catalysis neccesitates careful consideration of the particle size and structuralisation (e.g. pelletisation, surface-anchoring) of a material. Recently, particle size has been shown to dramatically alter the phys. and structural properties of certain MOFs but overall there is limited information on how the particle size affects the properties of flexible MOFs. Here we demonstrate that the particle size of a flexible MOF, specifically the as-synthesized form of [Cu(bcppm)H2O]•S (H2bcppm = bis(4-(4-carboxyphenyl)-1H-pyrazolyl)methane, S = solvent) (1), correlates with the rate of structural reorganisation from a "kinetically-trapped" activated 3D form of this MOF to the "open" 2D form of the structure. We also outline two methods for synthetically reducing the particle size of 1 at room temp., using 0.1 M NaOH (for two reaction times: 0.5 and 16 h) and with the sodium salt of the ligand Na2bcppm, producing crystals of 85 ± 15, 280 ± 14 and 402 ± 41 nm, resp. [on SciFinder(R)]Oliver M. Linder-Patton, Witold M. Bloch, Campbell J. Coghlan, Kenji Sumida, Susumu Kitagawa, Shuhei Furukawa, Christian J. Doonan and Christopher J. Sumb

Methods and strategies for gene structure curation in WormBase

The Caenorhabditis elegans genome sequence was published over a decade ago; this was the first published genome of a multi-cellular organism and now the WormBase project has had a decade of experience in curating this genome's sequence and gene structures. In one of its roles as a central repository for nematode biology, WormBase continues to refine the gene structure annotations using sequence similarity and other computational methods, as well as information from the literature- and community-submitted annotations. We describe the various methods of gene structure curation that have been tried by WormBase and the problems associated with each of them. We also describe the current strategy for gene structure curation, and introduce the WormBase ‘curation tool’, which integrates different data sources in order to identify new and correct gene structures

Policy ideas through the prism of knowledge regimes and framing

Policymakers are often confronted with problems that involve ambiguity and uncertainty (Zahariadis, 2003). In order to make sense of such problems and to identify possible solutions, they are on the lookout for policy ideas

Plasma Metabolomics Implicates Modified Transfer RNAs and Altered Bioenergetics in the Outcomes of Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a heterogeneous disorder with high mortality. METHODS: We conducted a comprehensive study of plasma metabolites using ultraperformance liquid chromatography mass spectrometry to identify patients at high risk of early death, to identify patients who respond well to treatment, and to provide novel molecular insights into disease pathogenesis. RESULTS: Fifty-three circulating metabolites distinguished well-phenotyped patients with idiopathic or heritable PAH (n=365) from healthy control subjects (n=121) after correction for multiple testing (P<7.3e-5) and confounding factors, including drug therapy, and renal and hepatic impairment. A subset of 20 of 53 metabolites also discriminated patients with PAH from disease control subjects (symptomatic patients without pulmonary hypertension, n=139). Sixty-two metabolites were prognostic in PAH, with 36 of 62 independent of established prognostic markers. Increased levels of tRNA-specific modified nucleosides (N2,N2-dimethylguanosine, N1-methylinosine), tricarboxylic acid cycle intermediates (malate, fumarate), glutamate, fatty acid acylcarnitines, tryptophan, and polyamine metabolites and decreased levels of steroids, sphingomyelins, and phosphatidylcholines distinguished patients from control subjects. The largest differences correlated with increased risk of death, and correction of several metabolites over time was associated with a better outcome. Patients who responded to calcium channel blocker therapy had metabolic profiles similar to those of healthy control subjects. CONCLUSIONS: Metabolic profiles in PAH are strongly related to survival and should be considered part of the deep phenotypic characterization of this disease. Our results support the investigation of targeted therapeutic strategies that seek to address the alterations in translational regulation and energy metabolism that characterize these patients

Steady-state modulation of voltage-gated K+ channels in rat arterial smooth muscle by cyclic AMP-dependent protein kinase and protein phosphatase 2B

Voltage-gated potassium channels (Kv) are important regulators of membrane potential in vascular smooth muscle cells, which is integral to controlling intracellular Ca2+ concentration and regulating vascular tone. Previous work indicates that Kv channels can be modulated by receptor-driven alterations of cyclic AMP-dependent protein kinase (PKA) activity. Here, we demonstrate that Kv channel activity is maintained by tonic activity of PKA. Whole-cell recording was used to assess the effect of manipulating PKA signalling on Kv and ATP-dependent K+ channels of rat mesenteric artery smooth muscle cells. Application of PKA inhibitors, KT5720 or H89, caused a significant inhibition of Kv currents. Tonic PKA-mediated activation of Kv appears maximal as application of isoprenaline (a β-adrenoceptor agonist) or dibutyryl-cAMP failed to enhance Kv currents. We also show that this modulation of Kv by PKA can be reversed by protein phosphatase 2B/calcineurin (PP2B). PKA-dependent inhibition of Kv by KT5720 can be abrogated by pre-treatment with the PP2B inhibitor cyclosporin A, or inclusion of a PP2B auto-inhibitory peptide in the pipette solution. Finally, we demonstrate that tonic PKA-mediated modulation of Kv requires intact caveolae. Pre-treatment of the cells with methyl-β-cyclodextrin to deplete cellular cholesterol, or adding caveolin-scaffolding domain peptide to the pipette solution to disrupt caveolae-dependent signalling each attenuated PKA-mediated modulation of the Kv current. These findings highlight a novel, caveolae-dependent, tonic modulatory role of PKA on Kv channels providing new insight into mechanisms and the potential for pharmacological manipulation of vascular tone

Exploring the relationship between homosexuality and sport among the teammates of a small, Midwestern Catholic college soccer team.

Despite decreasing homophobia, openly gay male athletes are still rare in organized, competitive teamsports. In this action research, we explore two aspects of homosexuality and sport: (1) the effect of a gay male soccer player coming out to his teammates; and (2) the effect of having an openly gay researcher in the field. This is, therefore, the first-ever first-hand account of an athlete's coming-out process with researchers in the field. Even though this is action research and, therefore, not generalizable, we highlight that this research contributes to the body of literature on sexuality and sport because we document the interactions of straight athletes with a gay player and a gay researcher among the heterosexual players at a small, Catholic college in the American Midwest. We use interviews to show that players were accepting of homosexuality before the beginning of this research and show that discussions with these two gay men further promoted players' perspectives on homosexuality. This led to an increase in the team's social cohesion and a decrease in heteronormativity

Working towards an engagement turn to agricultural research in the Tonle Sap Biosphere,Cambodia

A new generation of agricultural research programs are embracing use of participation as a vehicle for achieving greater impact and supporting transformative change in complex social-ecological systems. In this paper, we share learning from use of participatory action research in the Tonle Sap biosphere in Cambodia, as the main implementing methodology within a large multi-partner agricultural research program. We describe the program’s espoused approach to applying participatory methodologies focusing on co-ownership, equity and reflexivity with stakeholders throughout the research process. We then reflect upon our practice as we pursued initiatives to support increased income and nutrition outcomes for the poorest people in a diverse aquatic agricultural system characterized by inequality. We discuss the challenges and early successes of the process and share three enabling conditions that support a shift towards quality of participation in agricultural research: (1) focusing at the outset on a strengthsbased mind-set, (2) staging a critical stance to progressively build equity in process and outcomes, and (3) institutionalizing reflexivity to facilitate ongoing learning